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added test & corrected cram input

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This commit is contained in:
SusiJo 2022-05-20 09:13:27 +02:00
parent 5a1297cc7d
commit 3d57caa683
2 changed files with 38 additions and 14 deletions
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19
tests/modules/cnvkit/batch/main.nf
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@ -35,8 +35,8 @@ workflow test_cnvkit_cram {
input = [ input = [
[ id:'test'], // meta map [ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
] ]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
@ -53,5 +53,18 @@ workflow test_cnvkit_tumoronly {
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true) reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
CNVKIT_TUMORONLY ( input, [], [], reference ) CNVKIT_TUMORONLY ( input, fasta, [], reference )
}
workflow test_cnvkit_tumoronly_cram {
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
CNVKIT_TUMORONLY ( input, fasta, [], reference )
} }

33
tests/modules/cnvkit/batch/test.yml
View file

@ -1,15 +1,15 @@
- name: cnvkit batch test_cnvkit_hybrid - name: cnvkit batch test_cnvkit_hybrid
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
tags: tags:
- cnvkit/batch
- cnvkit - cnvkit
- cnvkit/batch
files: files:
- path: output/cnvkit/baits.antitarget.bed - path: output/cnvkit/baits.antitarget.bed
md5sum: d41d8cd98f00b204e9800998ecf8427e md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/cnvkit/baits.target.bed - path: output/cnvkit/baits.target.bed
md5sum: 26d25ff2d6c45b6d92169b3559c6acdb md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
- path: output/cnvkit/reference.cnn - path: output/cnvkit/reference.cnn
md5sum: ac99c1ad8b917b96ae15119146c91ab9 md5sum: 035d031f54c5f1b43b903da96559b475
- path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
md5sum: 203caf8cef6935bb50b4138097955cb8 md5sum: 203caf8cef6935bb50b4138097955cb8
- path: output/cnvkit/test.paired_end.sorted.bintest.cns - path: output/cnvkit/test.paired_end.sorted.bintest.cns
@ -28,10 +28,10 @@
md5sum: aa8a018b1d4d1e688c9f9f6ae01bf4d7 md5sum: aa8a018b1d4d1e688c9f9f6ae01bf4d7
- name: cnvkit batch test_cnvkit_wgs - name: cnvkit batch test_cnvkit_wgs
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
tags: tags:
- cnvkit/batch
- cnvkit - cnvkit
- cnvkit/batch
files: files:
- path: output/cnvkit/genome.antitarget.bed - path: output/cnvkit/genome.antitarget.bed
md5sum: d41d8cd98f00b204e9800998ecf8427e md5sum: d41d8cd98f00b204e9800998ecf8427e
@ -40,7 +40,7 @@
- path: output/cnvkit/genome.target.bed - path: output/cnvkit/genome.target.bed
md5sum: a13353ae9c8405e701390c069255bbd2 md5sum: a13353ae9c8405e701390c069255bbd2
- path: output/cnvkit/reference.cnn - path: output/cnvkit/reference.cnn
md5sum: 05c6211e0179885b8a83e44fd21d5f86 md5sum: 1606a85410bfaa79464be6e98699aa83
- path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
md5sum: 203caf8cef6935bb50b4138097955cb8 md5sum: 203caf8cef6935bb50b4138097955cb8
- path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn - path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
@ -59,10 +59,10 @@
md5sum: 6ae6b3fce7299eedca6133d911c38fe1 md5sum: 6ae6b3fce7299eedca6133d911c38fe1
- name: cnvkit batch test_cnvkit_cram - name: cnvkit batch test_cnvkit_cram
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
tags: tags:
- cnvkit/batch
- cnvkit - cnvkit
- cnvkit/batch
files: files:
- path: output/cnvkit/genome.antitarget.bed - path: output/cnvkit/genome.antitarget.bed
md5sum: d41d8cd98f00b204e9800998ecf8427e md5sum: d41d8cd98f00b204e9800998ecf8427e
@ -71,7 +71,7 @@
- path: output/cnvkit/genome.target.bed - path: output/cnvkit/genome.target.bed
md5sum: a13353ae9c8405e701390c069255bbd2 md5sum: a13353ae9c8405e701390c069255bbd2
- path: output/cnvkit/reference.cnn - path: output/cnvkit/reference.cnn
md5sum: 05c6211e0179885b8a83e44fd21d5f86 md5sum: 1606a85410bfaa79464be6e98699aa83
- path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn - path: output/cnvkit/test.paired_end.sorted.antitargetcoverage.cnn
md5sum: 203caf8cef6935bb50b4138097955cb8 md5sum: 203caf8cef6935bb50b4138097955cb8
- path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn - path: output/cnvkit/test.paired_end.sorted.targetcoverage.cnn
@ -90,10 +90,21 @@
md5sum: 6ae6b3fce7299eedca6133d911c38fe1 md5sum: 6ae6b3fce7299eedca6133d911c38fe1
- name: cnvkit batch test_cnvkit_tumoronly - name: cnvkit batch test_cnvkit_tumoronly
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
tags: tags:
- cnvkit/batch
- cnvkit - cnvkit
- cnvkit/batch
files:
- path: output/cnvkit/reference.antitarget-tmp.bed
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/cnvkit/reference.target-tmp.bed
md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
- name: cnvkit batch test_cnvkit_tumoronly_cram
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
tags:
- cnvkit
- cnvkit/batch
files: files:
- path: output/cnvkit/reference.antitarget-tmp.bed - path: output/cnvkit/reference.antitarget-tmp.bed
md5sum: d41d8cd98f00b204e9800998ecf8427e md5sum: d41d8cd98f00b204e9800998ecf8427e